Being out of sync now and then isn't a massive deal (we have this with Aspyr Media ports now and then), since you said it yourself the foundation is there, so they will already know what they are doing each time.
I think the single main issue here is BattleEye, which I hope you/VP can work on supporting on Linux together. Being out of sync for a small time is fine, but when it is in sync and you have limited server choice will probably be an issue.
As for this limitation "Limited User-Generated Content compatibility", this is an issue with any game on Steam FYI, but usually it all works fine. That's not really a limitation, as you cannot control workshop authors. So personally, I don't see that being an issue.
I did try two different user created Scenarios and both instantly crashed the game, the crash reporter VP uses claims the reports were sent, so hopefully they got them.